Framework for Machine Automation in Semiconductor Industry

Cílem diplomové práce bylo na základně existujících aplikací pro automatizaci strojů v polovodičovém průmyslu vytvořit analýzu současného stavu. Dle ní poté identifikovat části s opakující se funkcionalitou, nebo části náchylné k programátorským a uživatelským chybám. Poté pro tyto části vytvořit pře použitelnou implementaci, která by jako celek mohla sloužit jako framework pro automatizaci těchto strojů a díky tomu dosáhnou rychlejšího vývoje a spolehlivějších aplikací. Práce bude realizovaná v interpretovaném programovacím jazyce Java, díky své přenositelnosti a popularitě. Během vývoje bude kladen důraz na výslednou spolehlivost řešení a použití ověřených postupů.Goal of this thesis was to create analysis of current applications used for factory automation. Find parts with duplicate functionality, or parts prone to errors caused by developer or application user. Create new implementation for these cases, which will be more generic and as such usable as framework for factory automation. This approach should lead to shorter development cycle and more reliable automation software. Thesis is going to be implemented in Java programing language, thanks to its portability and popularity. During development primary goal is going to be reliability of final product as well as usage of already proven procedures.460 - Katedra informatikyvýborn

Framework for Board Games Realization on Computer

Práce si klade za cíl vytvořit interpret a uložení herních prvků. Jejím primárním cílem je vytvořit platformu pro tvorbu deskových her, která bude použitelná i člověkem, který nemá znalosti z oboru programování. Sekundárními cíli projektu je multiplatformní řešení, včetně možné komunikace dvou různých platforem, přenositelnost editorem vytvořených definic deskových her a uložení veškerých vytvořených dat v podobě čitelné člověkem.Work aims to create Board games interpreter and repository of game elements. The primary goal of work is to create a platform for board game realization, witch can be used also by someone who does not have knowledge in the field of programming. Secondary objectives of the project is a cross-platform solution, including possible communication between two different platforms, portability of created board game definitions and store of all data in human-readable form.

High-quality and universal empirical atomic charges for chemoinformatics applications.

BackgroundPartial atomic charges describe the distribution of electron density in a molecule and therefore provide clues to the chemical behaviour of molecules. Recently, these charges have become popular in chemoinformatics, as they are informative descriptors that can be utilised in pharmacophore design, virtual screening, similarity searches etc. Especially conformationally-dependent charges perform very successfully. In particular, their fast and accurate calculation via the Electronegativity Equalization Method (EEM) seems very promising for chemoinformatics applications. Unfortunately, published EEM parameter sets include only parameters for basic atom types and they often miss parameters for halogens, phosphorus, sulphur, triple bonded carbon etc. Therefore their applicability for drug-like molecules is limited.ResultsWe have prepared six EEM parameter sets which enable the user to calculate EEM charges in a quality comparable to quantum mechanics (QM) charges based on the most common charge calculation schemes (i.e., MPA, NPA and AIM) and a robust QM approach (HF/6-311G, B3LYP/6-311G). The calculated EEM parameters exhibited very good quality on a training set ([Formula: see text]) and also on a test set ([Formula: see text]). They are applicable for at least 95 % of molecules in key drug databases (DrugBank, ChEMBL, Pubchem and ZINC) compared to less than 60 % of the molecules from these databases for which currently used EEM parameters are applicable.ConclusionsWe developed EEM parameters enabling the fast calculation of high-quality partial atomic charges for almost all drug-like molecules. In parallel, we provide a software solution for their easy computation (http://ncbr.muni.cz/eem_parameters). It enables the direct application of EEM in chemoinformatics

Final report on deployment of consolidated platform and the overall architecture

This document is the final report about the activities of the Work Package 4 (WP4), aiming at provisioning a consistent e-infrastructure gradually integrating the existing isolated software solutions in the structural biology field into a single computing and data processing environment, based on the state of the art grid and cloud open source software tools and frameworks. This report follows the documents D4.3, MS14, D4.5 and MS15, respectively delivered at project month 15, 24, 26, 34, so that mostly the progress achieved until project month 36 not already described in the previous D4.5 ten months ago will be reported here, with references to MS15 when possible. The document starts with an updated description of the resources potentially available for the project from the EGI e-infrastructure, on top of which we built the consolidated West-Life platform. It then presents a detailed view of resource usage and their geographical distribution in the third and last year of the project, as obtained from the EGI Accounting Portal. The remaining of the document reports in details the final achievements about the three main aspects of the platform: the consolidated job management mechanism, the programmatic access to datasets and the unified security and accounting model

Parametrizace ekvalizace elektronegativity metodou diferenciální evoluce

Abstrakt formou posteru popisuje řešení parametrizace pro metodu ekvalizace elektronegativity pomocí metody diferenciální evoluce. Pomocí ní jsme dosáhli výrazně přesnějších výsledků i na heterogenních tréninkových sadách než se současným přístupem pomocí metody nejmenších čtverců.Abstrakt formou posteru popisuje řešení parametrizace pro metodu ekvalizace elektronegativity pomocí metody diferenciální evoluce. Pomocí ní jsme dosáhli výrazně přesnějších výsledků i na heterogenních tréninkových sadách než se současným přístupem pomocí metody nejmenších čtverců.Abstract presented as a poster describes parametrization of Electronegativity equalization method through differential evolution. We achieved more accurate results even for heterogeneous training sets than with common least squares method

Onedata4Sci: Life science data management solution based on Onedata

Life-science experimental methods generate vast and ever-increasing volumes of data, which provide highly valuable research resources. However, management of these data is nontrivial and applicable software solutions are currently subject to intensive development. The solutions mainly fall into one of the two groups: general data management systems (e.g. Onedata, iRODS, B2SHARE, CERNBox) or very specialised data management solutions (e.g. solutions for biomolecular simulation data, biological imaging data, genomic data). To bridge this gap between them, we provide Onedata4Sci, a prototype data management solution, which is focused on the management of life science data and covers four key steps of the data life cycle, i.e. data acquisition, user access, computational processing and archiving. Onedata4Sci is based on the Onedata data management system. It is written in Python, fully containerised, with the support for processing the stored data in Kubernetes. The applicability of Onedata4Sci is shown in three distinct use cases -- plant imaging data, cellular imaging data, and cryo-electron microscopy data. Despite the use cases covering very different types of data and user patterns, Onedata4Sci demonstrated an ability to successfully handle all these conditions. Complete source codes of Onedata4Sci are available on GitHub (https://github.com/CERIT-SC/onedata4sci), and its documentation and manual for installation are also provided

Quality of online information on breast cancer treatment options

Offering breast cancer patients treatment choice has become a priority as the involvement of patients in the decision-making process is associated with improved physical and psychological outcomes. As the Internet is increasingly being used by patients as a source of medical information, it is important to evaluate the quality of information relating to breast cancer on the Internet. We analysed 200 websites returned by google.co.uk searching “breast cancer treatment options” in terms of their typology and treatment options described. These were related to standard measures of health information quality such as the JAMA score and the presence of quality certifications, as well as readability. We found that health portals were of higher quality whilst commercial and professional websites were of poorer quality in terms of JAMA criteria. Overall, readability was higher than previously reported for other conditions, and Google ranked websites with better readability higher. Most websites discussed surgical and medical treatments. Few websites, with a large proportion being of commercial typology, discussed complementary and alternative medicine. Google ranked professional websites low whilst websites from non-profit organizations were promoted in the ranking

A survey of the European Open Science Cloud services for expanding the capacity and capabilities of multidisciplinary scientific applications

Open Science is a paradigm in which scientific data, procedures, tools and results are shared transparently and reused by society as a whole. The initiative known as the European Open Science Cloud (EOSC) is an effort in Europe to provide an open, trusted, virtual and federated computing environment to execute scientific applications, and to store, share and re-use research data across borders and scientific disciplines. Additionally, scientific services are becoming increasingly data-intensive, not only in terms of computationally intensive tasks but also in terms of storage resources. Computing paradigms such as High Performance Computing (HPC) and Cloud Computing are applied to e-science applications to meet these demands. However, adapting applications and services to these paradigms is not a trivial task, commonly requiring a deep knowledge of the underlying technologies, which often constitutes a barrier for its uptake by scientists in general. In this context, EOSC-SYNERGY, a collaborative project involving more than 20 institutions from eight European countries pooling their knowledge and experience to enhance EOSC\u27s capabilities and capacities, aims to bring EOSC closer to the scientific communities. This article provides a summary analysis of the adaptations made in the ten thematic services of EOSC-SYNERGY to embrace this paradigm. These services are grouped into four categories: Earth Observation, Environment, Biomedicine, and Astrophysics. The analysis will lead to the identification of commonalities, best practices and common requirements, regardless of the thematic area of the service. Experience gained from the thematic services could be transferred to new services for the adoption of the EOSC ecosystem framework

Molecular models superposition and visualization

A visualization system of molecular behaviour is presented in this paper. The system was designed for very large input data sets. An essential problem of the visualization is finding the best match of two structures. A solution (the superposition transformation) is discussed in detail